RetrogeneDB ID: retro_mmul_1532

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:115539304..115540428(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000022267
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSMMUG00000000801
• Aliases: None
• Description: transmembrane protein 183A [Source:RefSeq peptide;Acc:NP_001253210]

Sequence

>retro_mmul_1532
GCCGGCGGAACCGGCCTGCTAGGCAGGCCTCGCCCCAATACGGTCGCCGTGCCCAAGAGAGGAAAGCGACTCAAGTTCCG
GGCCCACGAAGCCTGCTCCGGCCGAGTGACCATGGCGGATTACGCCAAGTCGGATCCGGCTGTCATGAGATCTGGACGAG
TCAAGAAAACCGTAACCAACGCTGTTCAGCAGGAAGTAAAATCTCTTTGTGGTTTGGAAGCCTCTCAGGTTCCTGCAGAG
GAAGCTCTTTCTGGGGCTGGTGAGCCCTGTGACATCATCGACAGCAGTGATGAGATGGATGCCCAGGAGGAAAGCATCCA
CGAGAGAACTGTCTCCAGAGAAAAGAAAAGCAAGAGGCACAAAGAAGAAGTGGACGGGGCTGGAGGAGAAGAGTATCCCA
TGGATATTTGGCTGTTGCTGGCCTCCTATATCCATCCTGAGGACATTGTGAATTTTTCCCTGATTTGTAAGAATGCCTGG
ACTGTCACTTGCACTGCTACTTTTTGGACCAGGTTGTACCGAAGGCACTACCCGCTGGATGTTCCCTGCCTTTGCGTCTG
CGACCAGAGTCAATGGAGAAGCTGCACTGTCTCTGGGCTTGTGTGATCCGATCTCTGTACCATATGTATGAGCCATTTGC
TGCTCGAATCTCCAAGAATCCAGCCATTCCAGAAAGCACCCCCAGCGCATTAAAGAATTCCAAATGCTTACTTTTCTGAT
GCAGAAAGATTGTTGGGAACAGACAGGAACCAATGTGGGAATTCAACTTCAAGTTCAAAAAACAGTCCCCTAGGTTAAAG
AGCAAGTGTACAGGAGGATTGCAGCCTCCCGTTCAGTAACAAGATGTTCATACCAATCCAGACCAGCACTGCTGCCTACT
GCAGGTCACCACCCTCAGTTTCATCTGTATTCCGATTGTCATGGGCATGATATTTACTCTGTTTACTATCAGTGTGAGCA
CGGACATGTGGCATCATCCAGTGAGACTGGTGTTCCAAGATTCCCCTGTCCATGGTGATCGGAAACTGCGCAGTGAGCAG
GGTGTGCAAGTCATCCTGGACCCAGTGCACAGCGTTCGGCTCTTTGACTGGTGGCATCCTCAGTACCCATTCTCCCTGAG
AGCA

Alignment

ORF - retro_mmul_1532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.49 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARGPGPLGRPRPDTVAMPKRGKRLKFRAHDACSGRVTVADYANSDPAVVRSGRVKKAVANAVQQEVKSLC
          A.G.G.LGRPRP.TVA.PKRGKRLKFRAH.ACSGRVT.ADYA.SDPAV.RSGRVKK.V.NAVQQEVKSLC
Retrocopy AGGTGLLGRPRPNTVAVPKRGKRLKFRAHEACSGRVTMADYAKSDPAVMRSGRVKKTVTNAVQQEVKSLC

Parental  GLEASQVPAEEALSGAGEPCDIIDSSDEMDAQEESIHERTVSRKKKSKRHKE-LDGAGGEEYPMDIWLLL
          GLEASQVPAEEALSGAGEPCDIIDSSDEMDAQEESIHERTVSR.KKSKRHKE..DGAGGEEYPMDIWLLL
Retrocopy GLEASQVPAEEALSGAGEPCDIIDSSDEMDAQEESIHERTVSREKKSKRHKEEVDGAGGEEYPMDIWLLL

Parental  ASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDA-SLPLRLRPESMEKLRCLRACVIRSLYHM
          ASYI.PEDIVNFSLICKNAWTVTCTA.FWTRLYRRHY.LD..SLPLRLRPESMEKL.CL.ACVIRSLYHM
Retrocopy ASYIHPEDIVNFSLICKNAWTVTCTATFWTRLYRRHYPLDV<SLPLRLRPESMEKLHCLWACVIRSLYHM

Parental  YEPFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSPRLKSKCTGGLQPPVQ
          YEPFAARISKNPAIPESTPS.LKNSKCLLF.CRKIVGNRQEPMWEFNFKFKKQSPRLKSKCTGGLQPPVQ
Retrocopy YEPFAARISKNPAIPESTPSALKNSKCLLF*CRKIVGNRQEPMWEFNFKFKKQSPRLKSKCTGGLQPPVQ

Parental  YEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRLVFQDSPVHGGRKLRSEQGV
          ..DVHTNPDQ.CCLLQVTTL.FI.IPIVMGMIFTLFTI.VSTDM.HH.VRLVFQDSPVHG.RKLRSEQGV
Retrocopy *QDVHTNPDQHCCLLQVTTLSFICIPIVMGMIFTLFTISVSTDMWHHPVRLVFQDSPVHGDRKLRSEQGV

Parental  QVILDPVHSVRLFDWWHPQYPFSLRA
          QVILDPVHSVRLFDWWHPQYPFSLRA
Retrocopy QVILDPVHSVRLFDWWHPQYPFSLRA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.11 RPM	67.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	94.96 RPM
SRP007412_cerebellum	0.06 RPM	56.63 RPM
SRP007412_heart	0.00 RPM	14.90 RPM
SRP007412_kidney	0.12 RPM	39.67 RPM
SRP007412_liver	0.00 RPM	38.63 RPM
SRP007412_testis	0.11 RPM	64.87 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1532 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1532 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1532 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532 ,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,